[HTML][HTML] Fatty acid overproduction by gut commensal microbiota exacerbates obesity

T Takeuchi, K Kameyama, E Miyauchi, Y Nakanishi… - Cell metabolism, 2023‏ - cell.com
Although recent studies have highlighted the impact of gut microbes on the progression of
obesity and its comorbidities, it is not fully understood how these microbes promote these …

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing

RR Wick, LM Judd, KE Holt - PLOS Computational Biology, 2023‏ - journals.plos.org
A perfect bacterial genome assembly is one where the assembled sequence is an exact
match for the organism's genome—each replicon sequence is complete and contains no …

[HTML][HTML] ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs

H Yang, J Wu, X Huang, Y Zhou, Y Zhang, M Liu, Q Liu… - Nature, 2022‏ - nature.com
The composition of the intestinal microbiome varies considerably between individuals and is
correlated with health. Understanding the extent to which, and how, host genetics …

Ten common issues with reference sequence databases and how to mitigate them

SD Chorlton - Frontiers in Bioinformatics, 2024‏ - frontiersin.org
Metagenomic sequencing has revolutionized our understanding of microbiology. While
metagenomic tools and approaches have been extensively evaluated and benchmarked, far …

MOB-suite: software tools for clustering, reconstruction and ty** of plasmids from draft assemblies

J Robertson, JHE Nash - Microbial genomics, 2018‏ - microbiologyresearch.org
Large-scale bacterial population genetics studies are now routine due to cost-effective
Illumina short-read sequencing. However, analysing plasmid content remains difficult due to …

Complete, closed bacterial genomes from microbiomes using nanopore sequencing

EL Moss, DG Maghini, AS Bhatt - Nature biotechnology, 2020‏ - nature.com
Microbial genomes can be assembled from short-read sequencing data, but the assembly
contiguity of these metagenome-assembled genomes is constrained by repeat elements …

Unicycler: resolving bacterial genome assemblies from short and long sequencing reads

RR Wick, LM Judd, CL Gorrie… - PLoS computational …, 2017‏ - journals.plos.org
The Illumina DNA sequencing platform generates accurate but short reads, which can be
used to produce accurate but fragmented genome assemblies. Pacific Biosciences and …

Fitness Features Involved in the Biocontrol Interaction of Pseudomonas chlororaphis With Host Plants: The Case Study of PcPCL1606

E Arrebola, S Tienda, C Vida, A de Vicente… - Frontiers in …, 2019‏ - frontiersin.org
The goal of this mini review is to summarize the relevant contribution of some beneficial
traits to the behavior of the species Pseudomonas chlororaphis, and using that information …

Mutant phenotypes for thousands of bacterial genes of unknown function

MN Price, KM Wetmore, RJ Waters, M Callaghan… - Nature, 2018‏ - nature.com
One-third of all protein-coding genes from bacterial genomes cannot be annotated with a
function. Here, to investigate the functions of these genes, we present genome-wide mutant …

Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae

S O'donnell, JX Yue, OA Saada, N Agier, C Caradec… - Nature Genetics, 2023‏ - nature.com
Pangenomes provide access to an accurate representation of the genetic diversity of
species, both in terms of sequence polymorphisms and structural variants (SVs). Here we …